Highly Sensitive Chemigenetic FRET-Based Kinase Biosensors

Abstract

Fluorescent protein-based biosensors have transformed the study of cell physiology and pathology by enabling direct, live-cell measurements of biochemical activities with spatiotemporal precision. FRET-based biosensors offer a quantitative and well-defined readout mechanism popular among researchers, but have struggled to break free of characteristically low dynamic ranges and overall dependence on the cyan-yellow spectral region. Chemigenetic approaches that combine synthetic fluorophores with self-labeling protein tags represent an attractive solution to these longstanding constraints. Here, we pair different fluorescent protein donors with a HaloTag acceptor conjugated to a far-red fluorophore to obtain a suite of highly sensitive, chemigenetic FRET-based kinase activity biosensors with red-shifted emission and unprecedented dynamic range. We demonstrate the generalizability of this chemigenetic platform by developing biosensors for multiple kinases, as well as small GTPases and second messengers, all while maintaining high sensitivity. The high sensitivity and spectral tunability of these chemigenetic tools enabled us to perform robust multiplexed activity imaging of receptor-mediated signaling networks to quantitatively map isoform-specific coupling by GPCRs, as well as clear visualization of kinase activity in acute brain slices via two-photon fluorescence lifetime imaging. Our chemigenetic sensor toolkit thus provides the sensitivity and dimensionality needed to illuminate the spatiotemporal regulation of signaling networks in cells and tissues.